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Hoernlé was born in Secundra, Agra, British India on the 14th November,[1] the son of a Protestant missionary reverend, from a German family who had provided a number of recruits for the Church Missionary Society in the area. He descended from a long line of missionaries which included both linguists and revolutionaries; his father Christian Theophilus Hoernlé (1804–1882) translated the gospels into Kurdish and Urdu,[1] Hoernlé was therefore a British subject by birth; he was sent to Germany and his grandparents, at age 7, and was initially educated there.[1]

Hoernlé spent nearly his entire working life engaged in the study of Indo-Aryan languages and is perhaps best known for his decipherment of the Bower Manuscript collected by Hamilton Bower in Chinese Turkestan.[3][4] He was an early scholar of Khotanese.[5] Various super-powers were engaged in a competition to discover various archeological artifacts in Central Asia. Between 1895 and 1911, the Government of India gave Hoernlé a variety of manuscripts for him to decipher. He also took it upon himself to catalogue the Brahmi manuscripts that were sent to him by Aurel Stein. This is now referred to as the Hoernlé collection.[6]

Hoernlé was deceived by forgeries obtained by George Macartney and created by Islam Akhun. After a preliminary report in 1897, he published A Collection of Antiquities from Central Asia on these productions. The truth about these manuscripts was revealed to him by the explorer Sir Aurel Stein.[9] Hoernlé was deeply dismayed by his error, and attempted to acquire and destroy copies of his small book on these forgeries. Hoernlé's reputation survived this revelation, however, and his obituaries tactfully omitted the incident.[3]

In addition to his palaeographical and codicological work, Hoernlé published an important series of editions and studies on the history of medicine in South Asia, including a magisterial edition, translation and study of the Bower Manuscript.